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carlks library [309 articles]

Nye artikler sendt til carlks bibliotek.
  • Towards zoomable multidimensional maps of the cell
    Nature Biotechnology, Vol. 25, No. 5. (04 May 2007), pp. 547-554.
    by Zhenjun Hu, Joe Mellor, Jie Wu, Minoru Kanehisa, Joshua M Stuart, Charles Delisi
    posted to visualization by carlk on 2008-08-24 00:51:34 as ***** along with 10 people tmmurali kuhn cmmorel yas balajis thomaskelder dullhunk jyuh AlexanderPico Borelli
  • Genome-Wide Prediction of C. elegans Genetic Interactions
    Science, Vol. 311, No. 5766. (10 March 2006), pp. 1481-1484.
    by Weiwei Zhong, Paul W Sternberg
    posted to databases ssl worm by carlk on 2008-08-12 22:18:58 as ** along with 10 people and 3 groups nedwards tharris lp2 lfriedl indigoviolet xwbcn nirfriedman patrycjam patrycja_missiuro mingzhi C. elegans / WormBase kdl EisenLab
  • Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks
    Mol Syst Biol, Vol. 3 (17 April 2007)
    by Igor Ulitsky, Ron Shamir
    posted to networks ssl by carlk on 2008-08-12 06:10:29 as ** along with 2 people nicoleq zwang
  • Systematic genetic analysis with ordered arrays of yeast deletion mutants.
    Science, Vol. 294, No. 5550. (14 December 2001), pp. 2364-2368.
    by AH Tong, M Evangelista, AB Parsons, H Xu, GD Bader, N Pagé, M Robinson, S Raghibizadeh, CW Hogue, H Bussey, B Andrews, M Tyers, C Boone
    posted to ssl by carlk on 2008-08-12 05:50:22 as ** along with 7 people and 1 group shivaram lfriedl balajis opheliav nirfriedman blaine_5 ruvido kdl
  • Exploring genetic interactions and networks with yeast
    Nature Reviews Genetics, Vol. 8, No. 6., pp. 437-449.
    by Charles Boone, Howard Bussey, Brenda J Andrews
    posted to review ssl by carlk on 2008-08-12 05:46:55 as ** along with 5 people balajis zwang jyuh marck hryk
  • Calling on a million minds for community annotation in WikiProteins
    Genome Biology, Vol. 9, No. 5. (2008)
    by Barend Mons, Michael Ashburner, Christine Chichester, Erik van Mulligen, Marc Weeber, Johan den Dunnen, Gert J van Ommen, Mark Musen, Matthew Cockerill, Henning Hermjakob, Albert Mons, Abel Packer, Roberto Pacheco, Suzanna Lewis, Alfred Berkeley, William Melton, Nickolas Barris, Jimmy Wales, Gerard Meijssen, Erik Moeller, Peter Roes, Katy Borner, Amos Bairoch
    posted to wiki by carlk on 2008-08-12 03:43:20 as ** along with 17 people and 1 group jfr yas AlexanderPico thomaskelder dullhunk tharris renatomilani neils chad_davis fpattyn sjc Katje jamselem ChrisEvelo jyuh xingxu rholz microbiology_nijmegen
  • Defining genetic interaction
    Proceedings of the National Academy of Sciences, Vol. 105, No. 9. (4 March 2008), pp. 3461-3466.
    by Ramamurthy Mani, St, John L Hartman, Guri Giaever, Frederick P Roth
    posted to ssl by carlk on 2008-08-11 23:41:06 as ** along with 4 people tmmurali caseybrown jyuh inesdesantiago
  • Protein networks in disease
    Genome Research, Vol. 18, No. 4. (2008), pp. 644-652.
    by T Ideker, R Sharan
    posted to ssl by carlk on 2008-08-11 23:40:33 as **
  • Global Mapping of the Yeast Genetic Interaction Network
    Science, Vol. 303, No. 5659. (06 February 2004), pp. 808-813.
    by Amy HY Tong, Guillaume Lesage, Gary D Bader, Huiming Ding, Hong Xu, Xiaofeng Xin, James Young, Gabriel F Berriz, Renee L Brost, Michael Chang, Yiqun Chen, Xin Cheng, Gordon Chua, Helena Friesen, Debra S Goldberg, Jennifer Haynes, Christine Humphries, Grace He, Shamiza Hussein, Lizhu Ke, Nevan Krogan, Zhijian Li, Joshua N Levinson, Hong Lu, Patrice Menard, Christella Munyana, Ainslie B Parsons, Owen Ryan, Raffi Tonikian, Tania Roberts, Anne-Marie Sdicu, Jesse Shapiro, Bilal Sheikh, Bernhard Suter, Sharyl L Wong, Lan V Zhang, Hongwei Zhu, Christopher G Burd, Sean Munro, Chris Sander, Jasper Rine, Jack Greenblatt, Matthias Peter, Anthony Bretscher, Graham Bell, Frederick P Roth, Grant W Brown, Brenda Andrews, Howard Bussey, Charles Boone
    posted to experimental ssl yeast by carlk on 2008-08-11 23:36:44 as ** along with 20 people and 2 groups czeller ldfu pcahan1 lfriedl lyongu luispedro opheliav tabu Chue nirfriedman nickluscombe koller raiyar patrycjam patrycja_missiuro jiny chasmand tresch Takayuki ksiek kdl EBI-regulation
  • High-throughput, quantitative analyses of genetic interactions in E. coli.
    Nature methods (1 August 2008)
    by Athanasios Typas, Robert J J Nichols, Deborah A A Siegele, Michael Shales, Sean R R Collins, Bentley Lim, Hannes Braberg, Natsuko Yamamoto, Rikiya Takeuchi, Barry L L Wanner, Hirotada Mori, Jonathan S S Weissman, Nevan J J Krogan, Carol A A Gross
    posted to ssl by carlk on 2008-08-07 03:47:53 as ** along with 2 people nedwards jyuh
  • Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network
    Genome Biology, Vol. 5, No. 1. (2003)
    by Christine Brun, Francois Chevenet, David Martin, Jerome Wojcik, Alain Guenoche, Bernard Jacq
    posted to moduledetection modules by carlk on 2008-08-01 23:21:35 as ** along with 3 people gcalda jiny maralena
  • Protein complex prediction via cost-based clustering
    Bioinformatics, Vol. 20, No. 17. (22 November 2004), pp. 3013-3020.
    by AD King, N Przulj, I Jurisica
    posted to moduledetection modules by carlk on 2008-08-01 21:41:43 as ** along with 6 people and 1 group jiny lfriedl maralena hryk cerca ethkim kdl
  • Resolution limit in community detection
    Proc. Natl. Acad. Sci. USA, Vol. 104, No. 1. (2 January 2007), pp. 36-41.
    by Santo Fortunato, Marc Barthelemy
    edited by David O Siegmund
    posted to moduledetection modules by carlk on 2008-08-01 21:13:14 as ****
  • Subunit structure of gas vesicles: a MALDI-TOF mass spectrometry study.
    Biophysical journal, Vol. 86, No. 1 Pt 1. (January 2004), pp. 499-505.
    by M Belenky, R Meyers, J Herzfeld
    posted to gas_vessicle by carlk on 2008-07-31 18:07:38 as **
  • Predicting co-complexed protein pairs from heterogeneous data.
    PLoS computational biology, Vol. 4, No. 4. (April 2008)
    by J Qiu, WS Noble
    posted to complex complexes integration networks steiner by carlk on 2008-06-30 14:50:19 as ** along with 3 people bootsy mingzhi penpen926
  • Modelling antibody side chain conformations using heuristic database search.
    Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, Vol. 5 (1997), pp. 237-240.
    by DW Ritchie, GJ Kemp
    posted to protein scp by carlk on 2008-06-30 14:48:34 as **
  • Excluded volume in protein side-chain packing.
    J Mol Biol, Vol. 311, No. 1. (3 August 2001), pp. 183-193.
    by E Kussell, J Shimada, EI Shakhnovich
    posted to energy protein scp structure by carlk on 2008-06-30 14:47:13 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • Validation and refinement of gene-regulatory pathways on a network of physical interactions.
    Genome Biol, Vol. 6, No. 7. (2005)
    by CH Yeang, HC Mak, S McCuine, C Workman, T Jaakkola, T Ideker
    posted to networks pathways regulation regulatory by carlk on 2008-06-30 14:46:13 as ** along with 13 people and 1 group isimpson hplatero snuppepuppan abhik tmmurali textoris wnpx noano koller ccr cdppublications AlexanderPico jago CDP
  • Relating whole-genome expression data with protein-protein interactions.
    Genome Res, Vol. 12, No. 1. (January 2002), pp. 37-46.
    by R Jansen, D Greenbaum, M Gerstein
    posted to bicriteria expression linkprediction moduledetection modules networks by carlk on 2008-06-26 22:01:37 as ***** along with 8 people gurkanbebek gespim grahamc cjeans iris_2001 kintoki paolomarcatili nedwards
  • Integrative approach for computationally inferring protein domain interactions.
    Bioinformatics, Vol. 19, No. 8. (22 May 2003), pp. 923-929.
    by SK Ng, Z Zhang, SH Tan
    posted to domains linkprediction networks by carlk on 2008-06-26 20:59:34 as ** along with 3 people dyermd antonkratz phoenixzxl
  • Predicting protein-protein interactions using signature products
    Bioinformatics, Vol. 21, No. 2., 218.
    by Shawn Martin, Diana Roe, Jean-Loup Faulon
    posted to linkprediction networks by carlk on 2008-06-26 20:58:39 as ** along with 3 people mdimmic ziquje cjeans
  • Fitting protein chains to cubic lattice is NP-complete.
    Journal of bioinformatics and computational biology, Vol. 6, No. 1. (February 2008), pp. 93-106.
    by J Manuch, DR Gaur
    posted to lattice protein scp structure by carlk on 2008-06-26 19:05:51 as **
  • A Merge-Decoupling Dead End Elimination algorithm for protein side-chain conformation.
    International journal of data mining and bioinformatics, Vol. 1, No. 4. (2007), pp. 372-388.
    by KF Chong, HW Leong
    posted to algorithms protein scp structure by carlk on 2008-06-26 19:04:21 as **
  • Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains.
    Protein engineering, Vol. 8, No. 8. (August 1995), pp. 815-822.
    by I Lasters, M De Maeyer, J Desmet
    posted to algorithms protein scp structure by carlk on 2008-06-26 19:00:03 as **
  • A graph-theoretic algorithm for comparative modeling of protein structure.
    Journal of molecular biology, Vol. 279, No. 1. (29 May 1998), pp. 287-302.
    by R Samudrala, J Moult
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:59:24 as **
  • Critical assessment of side-chain conformational space sampling procedures designed for quantifying the effect of side-chain environment.
    Journal of computational chemistry, Vol. 24, No. 15. (30 November 2003), pp. 1950-1961.
    by R Gautier, P Tufféry
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:59:10 as **
  • A new approach to the rapid determination of protein side chain conformations.
    J Biomol Struct Dyn, Vol. 8, No. 6. (June 1991), pp. 1267-1289.
    by P Tuffery, C Etchebest, S Hazout, R Lavery
    posted to algorithms historical protein scp structure by carlk on 2008-06-26 18:58:46 as * along with 1 person dgront
  • Dead-end based modeling tools to explore the sequence space that is compatible with a given scaffold.
    Journal of protein chemistry, Vol. 16, No. 5. (July 1997), pp. 449-452.
    by I Lasters, J Desmet, M De Maeyer
    posted to algorithms energy protein scp structure by carlk on 2008-06-26 18:58:26 as **
  • Protein design automation.
    Protein Sci, Vol. 5, No. 5. (May 1996), pp. 895-903.
    by BI Dahiyat, SL Mayo
    posted to algorithms energy protein scp structure by carlk on 2008-06-26 18:57:55 as ** along with 2 people and 1 group shuns nknii TCR_Signaling
  • A new pairwise folding potential based on improved decoy generation and side-chain packing.
    Proteins, Vol. 54, No. 2. (1 February 2004), pp. 303-314.
    by C Loose, JL Klepeis, CA Floudas
    posted to energy protein scp structure by carlk on 2008-06-26 18:57:20 as **
  • Prediction and evaluation of side-chain conformations for protein backbone structures.
    Proteins, Vol. 26, No. 3. (November 1996), pp. 323-352.
    by PS Shenkin, H Farid, JS Fetrow
    posted to algorithms historical protein scp structure by carlk on 2008-06-26 18:56:52 as **
  • Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure.
    Biopolymers, Vol. 59, No. 2. (August 2001), pp. 72-86.
    by J Mendes, HA Nagarajaram, CM Soares, TL Blundell, MA Carrondo
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:56:29 as ** along with 1 person medic0747
  • Point matching under non-uniform distortions and protein side chain packing based on an efficient maximum clique algorithm.
    Genome informatics. International Conference on Genome Informatics, Vol. 13 (2002), pp. 143-152.
    by BK Dukka, T Akutsu, E Tomita, T Seki, A Fujiyama
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:54:29 as **
  • Determinants of protein side-chain packing.
    Protein science : a publication of the Protein Society, Vol. 3, No. 12. (December 1994), pp. 2358-2365.
    by R Tanimura, A Kidera, H Nakamura
    posted to protein scp structure by carlk on 2008-06-26 18:53:48 as **
  • The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins.
    Protein science : a publication of the Protein Society, Vol. 4, No. 11. (November 1995), pp. 2300-2309.
    by SY Chung, S Subbiah
    posted to protein scp structure virus by carlk on 2008-06-26 18:52:59 as **
  • Analysis of side-chain rotamers in transmembrane proteins.
    Biophysical journal, Vol. 87, No. 5. (November 2004), pp. 3460-3469.
    by AK Chamberlain, JU Bowie
    posted to protein scp structure by carlk on 2008-06-26 18:51:26 as ** along with 1 person and 1 group xdeupi LabCompMed
  • Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.
    J Mol Biol, Vol. 267, No. 5. (18 April 1997), pp. 1268-1282.
    by MJ Bower, FE Cohen, RL Dunbrack
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:50:21 as ** along with 5 people and 1 group kaarsinogen nknii blackbart mijam jwm TCR_Signaling
  • A graph-theory algorithm for rapid protein side-chain prediction.
    Protein Sci, Vol. 12, No. 9. (September 2003), pp. 2001-2014.
    by AA Canutescu, AA Shelenkov, RL Dunbrack
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:50:04 as ** along with 9 people karbak nigham bicko blackbart bluvsh1 rsantana mijam jwm newton1234
  • A tree-decomposition approach to protein structure prediction.
    Proc IEEE Comput Syst Bioinform Conf (2005), pp. 247-256.
    by J Xu, F Jiao, B Berger
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:49:50 as **** along with 1 person j3xucite
  • 1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap.
    J Comput Biol, Vol. 11, No. 1. (2004), pp. 27-52.
    by A Caprara, R Carr, S Istrail, G Lancia, B Walenz
    posted to alignment protein structure by carlk on 2008-06-26 18:34:32 as ** along with 2 people and 2 groups ana vavi structural_bioinformatics Bioinformatics
  • The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Ivelin Georgiev, Ryan H Lilien, Bruce R Donald
    posted to design protein scp structure by carlk on 2008-06-26 18:33:10 as ** along with 1 person RamuAnandakrishnan
  • Dead-end elimination for multistate protein design.
    Journal of computational chemistry, Vol. 28, No. 13. (October 2007), pp. 2122-2129.
    by C Yanover, M Fromer, JM Shifman
    posted to design protein scp structure by carlk on 2008-06-26 18:31:58 as **
  • Dead-end elimination with backbone flexibility.
    Bioinformatics (Oxford, England), Vol. 23, No. 13. (1 July 2007)
    by I Georgiev, BR Donald
    posted to scp structure by carlk on 2008-06-26 18:31:28 as ****
  • A reduction-based exact algorithm for the contact map overlap problem.
    Journal of computational biology : a journal of computational molecular cell biology, Vol. 14, No. 5. (June 2007), pp. 637-654.
    by W Xie, NV Sahinidis
    posted to alignment protein structure by carlk on 2008-06-26 18:30:29 as **
  • Matt: Local Flexibility Aids Protein Multiple Structure Alignment.
    PLoS Comput Biol, Vol. 4, No. 1. (11 January 2008)
    by Matthew Menke, Bonnie Berger, Lenore Cowen
    posted to alignment structure by carlk on 2008-06-26 18:29:44 as ** along with 2 people dimka marti
  • Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design.
    Bioinformatics (Oxford, England), Vol. 22, No. 14. (15 July 2006)
    by I Georgiev, RH Lilien, BR Donald
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:29:07 as **
  • Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach.
    Journal of bioinformatics and computational biology, Vol. 3, No. 1. (February 2005), pp. 103-126.
    by KC Dukka Bahadur, E Tomita, J Suzuki, T Akutsu
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:27:44 as **
  • Residue-rotamer-reduction algorithm for the protein side-chain conformation problem
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 188-194.
    by Wei Xie, Nikolaos V Sahinidis
    posted to algorithms protein scp structure by carlk on 2008-06-26 18:26:40 as ***** along with 3 people and 2 groups bicko marcius bluvsh1 BioinfoCIPF SGU-CIPF
  • Exploring conformational space using a mean field technique with MOLS sampling.
    Journal of biosciences, Vol. 32, No. 5. (August 2007), pp. 909-920.
    by PA Prasad, V Kanagasabai, J Arunachalam, N Gautham
    posted to algorithms energy protein scp structure by carlk on 2008-06-26 18:25:42 as *****
  • IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.
    Protein science : a publication of the Protein Society, Vol. 16, No. 7. (July 2007), pp. 1294-1307.
    by C Hartmann, I Antes, T Lengauer
    posted to algorithms protein scp search structure by carlk on 2008-06-26 18:24:57 as **
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